Database Setup

Files required

1. Loci table (tab-delimited); columns need:

   • Taxon_ID
   • Taxon_Name
   • Subtype*
   • Locus_Start
   • Locus_End
   • Operon_Start*
   • Operon_End*
   • Array_Start*
   • Array_End*
   • Array_status**
   • Operon_status***
   • Genbank_file
   • Array_File*
   • Fasta_File*
   • Author
   • File_Creation_Date*

"*" blank values allowed

"**" Possible values: "present", "absent"

"***" Possible values: "intact", "absent", "broken", "shuffled"

"broken" = some genes missing "shuffled" = gene order

1. Array table files (tab-delimited; copy and paste from CRISPRFinder); columns needed:

   • Start position
   • Direct repeat sequence
   • Spacer sequence
   • End position

2. Genbank files for each organism of interest

3. Fasta files of each genome (only needed genome sequence information is not included in the genbank files).

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Directory setup

The directory name for this example: './CLdb/' The example loci table: 'loci.txt'

$ mkdir CLdb
$ cd CLdb
$ mkdir genbank

• place/symlink genbank files in this directory

$ mkdir array

• place/symlink array files in this directory